A technique forinsitumeasurement of surface height variations in the scanning electron microscope (SEM) has been developed. Based on the comparison of images of microscopic areas obtained by tilting the electron beam, cross correlation is used to determine the image shift between like features in the stereo pair which is then used to dynamically correct the height of the tilt axis and lens focus in a feedback loop. This paper describes the principle of the method and its implementation using a commercial electron‐optical column. Experimental determination of measurement accuracy and examples of line scan profiling and three‐dimensional mapping are presented. Developments in instrumentation to further improve both accuracy and measurement speed are also discussed.